## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D18_supernatant_DMSO_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D18_supernatant_DMSO_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D18_supernatant_DMSO_3.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/slrinzema/tmp]    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false FLOW_MODE=false FLOW_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Oct 06 01:40:25 CEST 2023

## METRICS CLASS	picard.sam.DuplicationMetrics
LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
Unknown Library	542	25917013	14654514	0	423	3311234	0	0.12777	92589493

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	21226356	21226356
2.0	1.755849	1010199	1010199
3.0	2.327158	161457	161457
4.0	2.758981	66261	66261
5.0	3.085374	36502	36502
6.0	3.332078	22758	22758
7.0	3.518549	15485	15485
8.0	3.659493	11134	11134
9.0	3.766026	8355	8355
10.0	3.846549	6343	6343
11.0	3.907411	5184	5184
12.0	3.953415	3979	3979
13.0	3.988186	3384	3384
14.0	4.014468	2768	2768
15.0	4.034333	2340	2340
16.0	4.049349	2006	2006
17.0	4.060698	1724	1724
18.0	4.069276	1521	1521
19.0	4.07576	1360	1360
20.0	4.080661	1116	1116
21.0	4.084365	1038	1038
22.0	4.087165	920	920
23.0	4.089281	841	841
24.0	4.090881	749	749
25.0	4.09209	705	705
26.0	4.093004	602	602
27.0	4.093694	510	510
28.0	4.094217	510	510
29.0	4.094611	468	468
30.0	4.094909	423	423
31.0	4.095135	382	382
32.0	4.095305	345	345
33.0	4.095434	360	360
34.0	4.095531	319	319
35.0	4.095605	275	275
36.0	4.095661	262	262
37.0	4.095703	267	267
38.0	4.095735	200	200
39.0	4.095759	232	232
40.0	4.095777	195	195
41.0	4.09579	205	205
42.0	4.095801	191	191
43.0	4.095809	162	162
44.0	4.095815	164	164
45.0	4.095819	154	154
46.0	4.095822	146	146
47.0	4.095825	131	131
48.0	4.095827	133	133
49.0	4.095828	132	132
50.0	4.095829	118	118
51.0	4.09583	111	111
52.0	4.095831	128	128
53.0	4.095831	125	125
54.0	4.095832	100	100
55.0	4.095832	80	80
56.0	4.095832	85	85
57.0	4.095832	88	88
58.0	4.095833	83	83
59.0	4.095833	104	104
60.0	4.095833	78	78
61.0	4.095833	70	70
62.0	4.095833	72	72
63.0	4.095833	57	57
64.0	4.095833	88	88
65.0	4.095833	54	54
66.0	4.095833	60	60
67.0	4.095833	60	60
68.0	4.095833	57	57
69.0	4.095833	51	51
70.0	4.095833	62	62
71.0	4.095833	61	61
72.0	4.095833	56	56
73.0	4.095833	42	42
74.0	4.095833	53	53
75.0	4.095833	46	46
76.0	4.095833	46	46
77.0	4.095833	50	50
78.0	4.095833	50	50
79.0	4.095833	34	34
80.0	4.095833	41	41
81.0	4.095833	38	38
82.0	4.095833	33	33
83.0	4.095833	36	36
84.0	4.095833	36	36
85.0	4.095833	32	32
86.0	4.095833	33	33
87.0	4.095833	28	28
88.0	4.095833	29	29
89.0	4.095833	33	33
90.0	4.095833	21	21
91.0	4.095833	31	31
92.0	4.095833	30	30
93.0	4.095833	21	21
94.0	4.095833	34	34
95.0	4.095833	33	33
96.0	4.095833	23	23
97.0	4.095833	26	26
98.0	4.095833	26	26
99.0	4.095833	26	26
100.0	4.095833	21	21
101.0	0	18	18
102.0	0	25	25
103.0	0	20	20
104.0	0	19	19
105.0	0	19	19
106.0	0	24	24
107.0	0	15	15
108.0	0	20	20
109.0	0	17	17
110.0	0	22	22
111.0	0	16	16
112.0	0	22	22
113.0	0	19	19
114.0	0	19	19
115.0	0	11	11
116.0	0	16	16
117.0	0	18	18
118.0	0	16	16
119.0	0	17	17
120.0	0	19	19
121.0	0	10	10
122.0	0	12	12
123.0	0	23	23
124.0	0	21	21
125.0	0	10	10
126.0	0	17	17
127.0	0	14	14
128.0	0	14	14
129.0	0	16	16
130.0	0	11	11
131.0	0	12	12
132.0	0	21	21
133.0	0	17	17
134.0	0	15	15
135.0	0	18	18
136.0	0	13	13
137.0	0	9	9
138.0	0	7	7
139.0	0	10	10
140.0	0	15	15
141.0	0	9	9
142.0	0	11	11
143.0	0	8	8
144.0	0	12	12
145.0	0	12	12
146.0	0	10	10
147.0	0	12	12
148.0	0	11	11
149.0	0	2	2
150.0	0	10	10
151.0	0	7	7
152.0	0	8	8
153.0	0	5	5
154.0	0	6	6
155.0	0	11	11
156.0	0	9	9
157.0	0	9	9
158.0	0	16	16
159.0	0	9	9
160.0	0	7	7
161.0	0	8	8
162.0	0	9	9
163.0	0	14	14
164.0	0	12	12
165.0	0	7	7
166.0	0	5	5
167.0	0	10	10
168.0	0	14	14
169.0	0	8	8
170.0	0	7	7
171.0	0	5	5
172.0	0	8	8
173.0	0	5	5
174.0	0	5	5
175.0	0	10	10
176.0	0	9	9
177.0	0	10	10
178.0	0	9	9
179.0	0	3	3
180.0	0	5	5
181.0	0	6	6
182.0	0	10	10
183.0	0	2	2
184.0	0	2	2
185.0	0	5	5
186.0	0	5	5
187.0	0	6	6
188.0	0	4	4
189.0	0	7	7
190.0	0	5	5
191.0	0	4	4
192.0	0	5	5
193.0	0	8	8
194.0	0	10	10
195.0	0	5	5
196.0	0	6	6
197.0	0	5	5
198.0	0	7	7
199.0	0	7	7
200.0	0	4	4
201.0	0	2	2
202.0	0	5	5
203.0	0	3	3
204.0	0	4	4
205.0	0	3	3
206.0	0	5	5
207.0	0	4	4
208.0	0	7	7
209.0	0	5	5
210.0	0	5	5
211.0	0	1	1
212.0	0	3	3
213.0	0	6	6
214.0	0	7	7
215.0	0	9	9
216.0	0	5	5
217.0	0	4	4
218.0	0	6	6
219.0	0	5	5
220.0	0	3	3
221.0	0	7	7
222.0	0	5	5
223.0	0	7	7
225.0	0	7	7
226.0	0	4	4
227.0	0	3	3
228.0	0	5	5
229.0	0	5	5
230.0	0	4	4
231.0	0	2	2
232.0	0	2	2
233.0	0	4	4
234.0	0	6	6
235.0	0	1	1
236.0	0	5	5
237.0	0	5	5
238.0	0	4	4
239.0	0	3	3
240.0	0	2	2
241.0	0	4	4
242.0	0	3	3
243.0	0	6	6
244.0	0	5	5
245.0	0	3	3
246.0	0	1	1
247.0	0	6	6
248.0	0	8	8
249.0	0	1	1
250.0	0	3	3
251.0	0	2	2
252.0	0	3	3
253.0	0	4	4
254.0	0	2	2
255.0	0	5	5
256.0	0	3	3
257.0	0	2	2
258.0	0	3	3
259.0	0	2	2
260.0	0	5	5
261.0	0	1	1
262.0	0	3	3
263.0	0	1	1
264.0	0	4	4
265.0	0	4	4
266.0	0	3	3
267.0	0	4	4
268.0	0	2	2
269.0	0	2	2
270.0	0	2	2
271.0	0	4	4
272.0	0	2	2
273.0	0	4	4
274.0	0	5	5
275.0	0	4	4
276.0	0	1	1
278.0	0	1	1
279.0	0	1	1
280.0	0	3	3
282.0	0	1	1
283.0	0	4	4
284.0	0	3	3
285.0	0	1	1
286.0	0	1	1
287.0	0	3	3
288.0	0	1	1
289.0	0	1	1
290.0	0	2	2
291.0	0	2	2
292.0	0	1	1
293.0	0	1	1
294.0	0	1	1
295.0	0	3	3
296.0	0	1	1
297.0	0	2	2
298.0	0	1	1
299.0	0	1	1
300.0	0	2	2
301.0	0	3	3
303.0	0	2	2
304.0	0	2	2
305.0	0	1	1
306.0	0	2	2
307.0	0	2	2
308.0	0	1	1
309.0	0	1	1
310.0	0	1	1
311.0	0	1	1
312.0	0	1	1
313.0	0	4	4
316.0	0	1	1
317.0	0	1	1
318.0	0	3	3
319.0	0	2	2
320.0	0	3	3
321.0	0	3	3
322.0	0	2	2
323.0	0	1	1
325.0	0	2	2
326.0	0	3	3
327.0	0	2	2
328.0	0	2	2
329.0	0	3	3
330.0	0	1	1
332.0	0	2	2
333.0	0	2	2
334.0	0	4	4
335.0	0	3	3
337.0	0	1	1
338.0	0	1	1
339.0	0	1	1
341.0	0	2	2
342.0	0	4	4
345.0	0	1	1
346.0	0	1	1
348.0	0	1	1
352.0	0	2	2
353.0	0	1	1
355.0	0	1	1
356.0	0	2	2
359.0	0	2	2
361.0	0	1	1
362.0	0	1	1
363.0	0	2	2
365.0	0	1	1
366.0	0	1	1
367.0	0	3	3
369.0	0	1	1
371.0	0	1	1
375.0	0	1	1
377.0	0	1	1
379.0	0	1	1
381.0	0	2	2
385.0	0	1	1
387.0	0	1	1
388.0	0	1	1
389.0	0	3	3
391.0	0	2	2
392.0	0	1	1
393.0	0	1	1
394.0	0	1	1
396.0	0	1	1
397.0	0	1	1
398.0	0	1	1
399.0	0	1	1
401.0	0	1	1
402.0	0	2	2
403.0	0	1	1
404.0	0	1	1
405.0	0	2	2
406.0	0	1	1
408.0	0	1	1
409.0	0	1	1
412.0	0	2	2
413.0	0	1	1
415.0	0	1	1
418.0	0	1	1
419.0	0	2	2
423.0	0	1	1
424.0	0	1	1
428.0	0	1	1
429.0	0	1	1
432.0	0	2	2
433.0	0	2	2
434.0	0	1	1
435.0	0	1	1
440.0	0	2	2
441.0	0	1	1
442.0	0	2	2
443.0	0	1	1
444.0	0	2	2
448.0	0	1	1
451.0	0	1	1
453.0	0	3	3
454.0	0	1	1
457.0	0	1	1
460.0	0	1	1
464.0	0	2	2
465.0	0	1	1
466.0	0	1	1
467.0	0	1	1
468.0	0	2	2
469.0	0	1	1
471.0	0	2	2
473.0	0	1	1
474.0	0	1	1
475.0	0	2	2
476.0	0	2	2
482.0	0	1	1
484.0	0	2	2
492.0	0	3	3
494.0	0	1	1
497.0	0	4	4
499.0	0	3	3
500.0	0	1	1
501.0	0	1	1
503.0	0	1	1
506.0	0	1	1
513.0	0	1	1
514.0	0	1	1
516.0	0	1	1
521.0	0	1	1
524.0	0	1	1
525.0	0	1	1
531.0	0	1	1
532.0	0	1	1
534.0	0	1	1
535.0	0	1	1
539.0	0	1	1
540.0	0	1	1
541.0	0	1	1
550.0	0	1	1
557.0	0	1	1
559.0	0	1	1
560.0	0	1	1
561.0	0	1	1
562.0	0	1	1
564.0	0	1	1
565.0	0	2	2
572.0	0	2	2
575.0	0	1	1
586.0	0	1	1
591.0	0	1	1
592.0	0	2	2
594.0	0	1	1
602.0	0	2	2
606.0	0	1	1
610.0	0	1	1
617.0	0	1	1
622.0	0	1	1
625.0	0	1	1
626.0	0	1	1
628.0	0	1	1
640.0	0	1	1
646.0	0	1	1
647.0	0	1	1
658.0	0	1	1
668.0	0	1	1
673.0	0	1	1
687.0	0	1	1
701.0	0	1	1
703.0	0	1	1
714.0	0	1	1
717.0	0	1	1
719.0	0	1	1
726.0	0	1	1
731.0	0	1	1
781.0	0	1	1
795.0	0	1	1
806.0	0	1	1
895.0	0	1	1
898.0	0	1	1
907.0	0	1	1
908.0	0	2	2
914.0	0	1	1
917.0	0	1	1
949.0	0	1	1
984.0	0	1	1
1006.0	0	1	1
1015.0	0	1	1
1022.0	0	1	1
1051.0	0	1	1
1057.0	0	1	1
1081.0	0	1	1
1087.0	0	1	1
1090.0	0	1	1
1129.0	0	1	1
1130.0	0	1	1
1133.0	0	1	1
1189.0	0	1	1
1209.0	0	1	1
1225.0	0	1	1
1267.0	0	1	1
1304.0	0	1	1
1311.0	0	1	1
1336.0	0	1	1
1343.0	0	1	1
1349.0	0	1	1
1365.0	0	1	1
1413.0	0	1	1
1473.0	0	1	1
1498.0	0	1	1
1563.0	0	1	1
1684.0	0	1	1
2325.0	0	1	1
2838.0	0	1	1